How to train a sequence labeling model with annotations from three annotators?
Both ways are valid. It depends on what you want from the model and expect from the data. Generally though I would use 1 assumption and stick with it (unless there was a specific reason not to), so I would use all lines for test if training done that way, and same for majority.
Also note if you ever get more than 3 people, you can choose to do a variance based approach (use data if only x% agree, throw away otherwise (or you could even weigh controversial labels lower))